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- PDB-8znk: chromone glycosyltransferase (UGT93BB1,SdUGT2) -

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Basic information

Entry
Database: PDB / ID: 8znk
Titlechromone glycosyltransferase (UGT93BB1,SdUGT2)
Componentschromone glycosyltransferase (UGT93BB1)
KeywordsPLANT PROTEIN / glycosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesSaposhnikovia divaricata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZou, J.L. / Li, H.Y. / Wang, Z.L. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA0914100 China
CitationJournal: Nat Commun / Year: 2025
Title: Complete biosynthetic pathway of furochromones in Saposhnikovia divaricata and its evolutionary mechanism in Apiaceae plants.
Authors: Zou, J.L. / Li, H.Y. / Nie, B. / Wang, Z.L. / Zhao, C.X. / Tian, Y.G. / Lin, L.Q. / Xu, W.Z. / Hou, Z.W. / Sun, W.K. / Han, X.X. / Zhang, M. / Wang, H.T. / Li, Q.Y. / Wang, L. / Ye, M.
History
DepositionMay 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: chromone glycosyltransferase (UGT93BB1)
B: chromone glycosyltransferase (UGT93BB1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7594
Polymers105,9512
Non-polymers8082
Water9,494527
1
A: chromone glycosyltransferase (UGT93BB1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3792
Polymers52,9751
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chromone glycosyltransferase (UGT93BB1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3792
Polymers52,9751
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.560, 67.610, 93.850
Angle α, β, γ (deg.)90.00, 99.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein chromone glycosyltransferase (UGT93BB1)


Mass: 52975.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saposhnikovia divaricata (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 27% 3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→34.53 Å / Num. obs: 80838 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Χ2: 0.97 / Net I/σ(I): 12.7 / Num. measured all: 555217
Reflection shellResolution: 1.88→1.93 Å / % possible obs: 99.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.379 / Num. measured all: 39877 / Num. unique obs: 5848 / CC1/2: 0.573 / Rpim(I) all: 0.566 / Rrim(I) all: 1.492 / Χ2: 0.97 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→34.53 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 4020 4.97 %
Rwork0.187 --
obs0.1889 80820 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7062 0 50 527 7639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087293
X-RAY DIFFRACTIONf_angle_d1.1279916
X-RAY DIFFRACTIONf_dihedral_angle_d7.371977
X-RAY DIFFRACTIONf_chiral_restr0.0681112
X-RAY DIFFRACTIONf_plane_restr0.011270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90.32171330.26812544X-RAY DIFFRACTION100
1.9-1.930.3221280.26742663X-RAY DIFFRACTION99
1.93-1.950.30591220.25832602X-RAY DIFFRACTION99
1.95-1.980.31751310.25932664X-RAY DIFFRACTION100
1.98-20.28931430.24162610X-RAY DIFFRACTION99
2-2.030.26631150.22742669X-RAY DIFFRACTION100
2.03-2.060.25611520.21812633X-RAY DIFFRACTION99
2.06-2.090.26071400.21692596X-RAY DIFFRACTION100
2.09-2.130.25951390.21142636X-RAY DIFFRACTION99
2.13-2.160.24691310.20442648X-RAY DIFFRACTION100
2.16-2.20.24821230.20162630X-RAY DIFFRACTION99
2.2-2.250.23051370.20432650X-RAY DIFFRACTION100
2.25-2.290.26611470.1972643X-RAY DIFFRACTION100
2.29-2.340.25041230.2082665X-RAY DIFFRACTION100
2.34-2.40.25631430.20462628X-RAY DIFFRACTION100
2.4-2.460.23651430.20132660X-RAY DIFFRACTION100
2.46-2.520.25361560.1952622X-RAY DIFFRACTION100
2.52-2.60.24531640.19222630X-RAY DIFFRACTION100
2.6-2.680.22131440.19372648X-RAY DIFFRACTION100
2.68-2.780.20821340.19082648X-RAY DIFFRACTION100
2.78-2.890.23121310.18382674X-RAY DIFFRACTION100
2.89-3.020.22221480.18032646X-RAY DIFFRACTION100
3.02-3.180.19291510.18292652X-RAY DIFFRACTION100
3.18-3.380.21481260.17422693X-RAY DIFFRACTION100
3.38-3.640.20231300.17042667X-RAY DIFFRACTION100
3.64-40.19571510.1642671X-RAY DIFFRACTION100
4-4.580.19481210.15372692X-RAY DIFFRACTION100
4.58-5.770.19761440.17522704X-RAY DIFFRACTION100
5.77-34.530.22671700.18032712X-RAY DIFFRACTION99

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